knitr::opts_chunk$set(echo = FALSE)
### Create Output Directory ###
# if save_output = TRUE
if(params$save_output){
  outfile_dir <- file.path(params$output_dir,"EpiCompare_file")
  if(!dir.exists(outfile_dir)){
    dir.create(outfile_dir, showWarnings = FALSE, recursive = TRUE)
  }
}

#### ------ Prepare genome builds ------ ####
# e.g. genome_build <- list(reference="hg19",peakfiles="hg38",blacklist="hg19")
# or... genome_build <- "hg19"
builds <- prepare_genome_builds(genome_build = params$genome_build)
## Standardise all data to hg19 build 
output_build <- prepare_output_build(params$genome_build_output)

#### ------ Prepare peaklist(s) ------ ####
# and check that the list is named, if not default filenames are used 
peaklist <- prepare_peaklist(peaklist = params$peakfile) 
peaklist <- liftover_grlist(grlist = peaklist, 
                            input_build = builds$peaklist,
                            output_build = output_build)

#### ------ Prepare reference(s) ------ ####
reference <- prepare_reference(reference = params$reference)
reference <- liftover_grlist(grlist = reference, 
                            input_build = builds$reference,
                            output_build = output_build)

#### ------ Prepare blacklist ------ ####
blacklist <- liftover_grlist(grlist = params$blacklist,
                             input_build = builds$blacklist, 
                             output_build = output_build) 

### Standardise peaklist(s) ###
peaklist_tidy <- tidy_peakfile(peaklist = peaklist,
                               blacklist = blacklist)

### Standardise reference(s) ###
# and include in peaklist
reference_tidy <- reference
if (!is.null(reference)){
  reference_tidy <- tidy_peakfile(peaklist = reference,
                                  blacklist = blacklist)
  peaklist_tidy <- c(peaklist_tidy, reference_tidy)
}

### Obtain Genome Annotation ### 
txdb <- check_genome_build(genome_build = output_build)

### Dynamic Figure Height ###  
fig_height <- fig_length(default_size = 7,
                         number_of_items = length(peaklist_tidy),
                         max_items = 10)

EpiCompare compares epigenomic datasets for quality control and benchmarking purposes. The report consists of three sections:

  1. General Metrics: Metrics on peaks - percentage of blacklisted and non-standard peaks and peak widths - and fragments - duplication rate - of samples.
  2. Peak Overlap: Frequency, percentage, statistical significance of overlapping and non-overlapping peaks. This also includes Upset, precision-recall and correlation plots.
  3. Functional Annotation: Functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. This also includes peak enrichment around TSS.
Input Datasets
  • Reference peakfile: ENCODE_H3K27ac_Broad
  • Total of 18 peak files:
## [1] "File1: scTIP_Top01"
## [1] "File2: scTIP_Top02"
## [1] "File3: scTIP_Top03"
## [1] "File4: scTIP_Top04"
## [1] "File5: scTIP_Top05"
## [1] "File6: scTIP_Top06"
## [1] "File7: scTIP_Top07"
## [1] "File8: scTIP_Top08"
## [1] "File9: scTIP_Top09"
## [1] "File10: scTIP_Top10"
## [1] "File11: H3K27ac_Diagenode_pA_Tn5_F10_P9_R1"
## [1] "File12: H3K27ac_Abcam_Tn5_F6_P7_R1"
## [1] "File13: H3K27ac_Abcam_Tn5_F10_P7_R1"
## [1] "File14: H3K27ac_Abcam_pA_Tn5_F6_P9_R2"
## [1] "File15: H3K27ac_Abcam_pA_Tn5_F6_P9_R1"
## [1] "File16: H3K27ac_Abcam_pA_Tn5_F10_P9_R1"
## [1] "File17: H3K27ac_Abcam_pA_Tn5_F10_P6_R1"
## [1] "File18: ENCODE_H3K27ac_Broad"
Code

The function call used to create the report.

EpiCompare(peakfiles = list(scTIP_Top01, scTIP_Top02, scTIP_Top03, scTIP_Top04, scTIP_Top05, scTIP_Top06, scTIP_Top07, scTIP_Top08, scTIP_Top09, scTIP_Top10, H3K27ac_Diagenode_pA_Tn5_F10_P9_R1, H3K27ac_Abcam_Tn5_F6_P7_R1, H3K27ac_Abcam_Tn5_F10_P7_R1, H3K27ac_Abcam_pA_Tn5_F6_P9_R2, H3K27ac_Abcam_pA_Tn5_F6_P9_R1, H3K27ac_Abcam_pA_Tn5_F10_P9_R1, H3K27ac_Abcam_pA_Tn5_F10_P6_R1, ENCODE_H3K27ac_Broad),
           genome_build = hg38, hg38, hg38,
           genome_build_output = hg38,
           blacklist = blacklist,
           picard_files = list(),
           reference = ENCODE_H3K27ac_Broad,
           upset_plot = TRUE,
           stat_plot = TRUE,
           chromHMM_plot = TRUE,
           chromHMM_annotation = "K562",
           chipseeker_plot = TRUE,
           enrichment_plot = TRUE,
           tss_plot = TRUE,
           precision_recall_plot = FALSE,
           corr_plot=FALSE,
           interact = TRUE,
           save_output = TRUE,
           output_dir = "/Users/xindong/Downloads/H3K27ac_sc_top10")

1. General Metrics

Peak Information

Column Description:

  • PeakN before tidy: Total number of peaks including those blacklisted and those in non-standard chromosomes.
  • Blacklisted peaks removed (%): Percentage of blacklisted peaks in samples. E.g. ENCODE hg19 blacklist includes regions in the hg19 genome that have anomalous and/or unstructured signals independent of the cell-line or experiment.
  • Non-standard peaks removed (%): Percentage of peaks in non-standard and/or mitochondrial chromosomes. Identified using BRGenomics::tidyChromosomes().
  • PeakN after tidy: Total number of peaks after removing those in blacklisted regions and non-standard chromosomes.

NB: EpiCompare uses filtered peakfiles (i.e. datasets after removing peaks in blacklisted regions and non-standard chromosomes)


PeakN Before Tidy Blacklisted Peaks Removed (%) Non-standard Peaks Removed (%) PeakN After Tidy
scTIP_Top01 86202 0.1020 0.377 85789
scTIP_Top02 80201 0.0985 0.404 79798
scTIP_Top03 74447 0.1260 0.373 74075
scTIP_Top04 72356 0.1310 0.417 71959
scTIP_Top05 70543 0.1080 0.383 70197
scTIP_Top06 66915 0.1150 0.384 66581
scTIP_Top07 66596 0.1190 0.383 66262
scTIP_Top08 64614 0.1180 0.396 64282
scTIP_Top09 65089 0.1310 0.401 64743
scTIP_Top10 63056 0.1470 0.442 62684
H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 71682 0.1510 0.632 71121
H3K27ac_Abcam_Tn5_F6_P7_R1 99997 0.0770 0.426 99494
H3K27ac_Abcam_Tn5_F10_P7_R1 115270 0.1200 0.370 114706
H3K27ac_Abcam_pA_Tn5_F6_P9_R2 110709 0.1740 0.447 110021
H3K27ac_Abcam_pA_Tn5_F6_P9_R1 60064 0.0999 0.526 59688
H3K27ac_Abcam_pA_Tn5_F10_P9_R1 65526 0.1920 0.491 65078
H3K27ac_Abcam_pA_Tn5_F10_P6_R1 73765 0.2100 0.493 73246

Fragment Information

Metrics on fragments is shown only if Picard summary is provided. See manual for help.

Column Description:

  • Mapped_Fragments: Number of mapped read pairs in the file.
  • Duplication_Rate: Percentage of mapped sequence that is marked as duplicate.
  • Unique_Fragments: Number of mapped sequence that is not marked as duplicate.


Peak widths

Distribution of peak widths in samples


2. Peak Overlap

Percentage Overlap

Percentage of overlapping peaks between samples. Hover over heatmap for percentage values.

N.B. How to interpret heatmap: [Samples in x-axis of heatmap] peaks in [Samples in y-axis of heatmap] peaks


Upset Plot

Upset plot of overlapping peaks between samples. See here on how to interpret the plot.

Statistical Significance

Depending on the format of the reference file, EpiCompare outputs different plots:

  • Reference dataset has BED6+4 format (peak calling performed with MACS2): EpiCompare generates paired boxplot per sample showing the distribution of -log10(q-value) of reference peaks that are overlapping and non-overlapping with the sample dataset.
  • Reference dataset does not have BED6+4 format: EpiCompare generates a barplot of percentage of overlapping sample peaks with the reference, coloured by statistical significance (adjusted p-value) of the overlap.

Reference peakfile: ENCODE_H3K27ac_Broad

Keys:

  • Overlap: Sample peaks in Reference peaks
  • Unique: Sample peaks not in Reference peaks


Precision-Recall Curves

The first plot shows the balance between precision and recall across multiple peak calling stringency thresholds.

  • Precision: Number of sample peaks in reference.
  • Recall: Number of reference peaks in sample.

The second plot shows F1 score (a score that combines precision and recall) across the different peak calling stringency thresholds.

  • F1: 2*(precision*recall) / (precision+recall)
## NULL
## NULL

Correlation Plot

The correlation plot shows the correlation between the quantiles when the genome is binned at a set size. These quantiles are based on the intensity of the peak, dependent on the peak caller used (q-value for MACS2):

## NULL

3. Functional Annotation

3.1 ChromHMM

ChromHMM annotates and characterises peaks into different chromatin states. ChromHMM annotations used in EpiCompare were obtained from here.

  • Cell-type annotation file used in this analysis: K562

All samples

ChromHMM annotation of individual samples.

Overlap: Sample peaks in Reference peaks

Percentage of Sample peaks found in Reference peaks (Reference peakfile: ENCODE_H3K27ac_Broad)

query subject overlap total Percentage type peaklist1 peaklist2
scTIP_Top01 ENCODE_H3K27ac_Broad 33794 85789 39.4 precision scTIP_Top01 ENCODE_H3K27ac_Broad
scTIP_Top02 ENCODE_H3K27ac_Broad 32066 79798 40.2 precision scTIP_Top02 ENCODE_H3K27ac_Broad
scTIP_Top03 ENCODE_H3K27ac_Broad 32400 74075 43.7 precision scTIP_Top03 ENCODE_H3K27ac_Broad
scTIP_Top04 ENCODE_H3K27ac_Broad 29010 71959 40.3 precision scTIP_Top04 ENCODE_H3K27ac_Broad
scTIP_Top05 ENCODE_H3K27ac_Broad 28087 70197 40.0 precision scTIP_Top05 ENCODE_H3K27ac_Broad
scTIP_Top06 ENCODE_H3K27ac_Broad 26962 66581 40.5 precision scTIP_Top06 ENCODE_H3K27ac_Broad
scTIP_Top07 ENCODE_H3K27ac_Broad 26803 66262 40.5 precision scTIP_Top07 ENCODE_H3K27ac_Broad
scTIP_Top08 ENCODE_H3K27ac_Broad 25486 64282 39.6 precision scTIP_Top08 ENCODE_H3K27ac_Broad
scTIP_Top09 ENCODE_H3K27ac_Broad 25355 64743 39.2 precision scTIP_Top09 ENCODE_H3K27ac_Broad
scTIP_Top10 ENCODE_H3K27ac_Broad 26476 62684 42.2 precision scTIP_Top10 ENCODE_H3K27ac_Broad
H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 30758 71121 43.2 precision H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad 29293 99494 29.4 precision H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad 27299 114706 23.8 precision H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad 28186 110021 25.6 precision H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad 30942 59688 51.8 precision H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 28515 65078 43.8 precision H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad 28346 73246 38.7 precision H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 54625 54625 100.0 precision ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top01 19744 54625 36.1 recall scTIP_Top01 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top02 18942 54625 34.7 recall scTIP_Top02 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top03 19076 54625 34.9 recall scTIP_Top03 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top04 17722 54625 32.4 recall scTIP_Top04 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top05 17224 54625 31.5 recall scTIP_Top05 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top06 16617 54625 30.4 recall scTIP_Top06 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top07 16695 54625 30.6 recall scTIP_Top07 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top08 16027 54625 29.3 recall scTIP_Top08 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top09 15925 54625 29.2 recall scTIP_Top09 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top10 16512 54625 30.2 recall scTIP_Top10 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 40868 54625 74.8 recall H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1 48555 54625 88.9 recall H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1 51738 54625 94.7 recall H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2 51545 54625 94.4 recall H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1 38005 54625 69.6 recall H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1 43749 54625 80.1 recall H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1 46710 54625 85.5 recall H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 54625 54625 100.0 recall ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad

ChromHMM annotation of sample peaks found in reference peaks.

Overlap: Reference peaks in Sample peaks

Percentage of Reference peaks found in Sample peaks (Reference peakfile: ENCODE_H3K27ac_Broad)

query subject overlap total Percentage type peaklist1 peaklist2
ENCODE_H3K27ac_Broad scTIP_Top01 19744 54625 36.1 precision ENCODE_H3K27ac_Broad scTIP_Top01
ENCODE_H3K27ac_Broad scTIP_Top02 18942 54625 34.7 precision ENCODE_H3K27ac_Broad scTIP_Top02
ENCODE_H3K27ac_Broad scTIP_Top03 19076 54625 34.9 precision ENCODE_H3K27ac_Broad scTIP_Top03
ENCODE_H3K27ac_Broad scTIP_Top04 17722 54625 32.4 precision ENCODE_H3K27ac_Broad scTIP_Top04
ENCODE_H3K27ac_Broad scTIP_Top05 17224 54625 31.5 precision ENCODE_H3K27ac_Broad scTIP_Top05
ENCODE_H3K27ac_Broad scTIP_Top06 16617 54625 30.4 precision ENCODE_H3K27ac_Broad scTIP_Top06
ENCODE_H3K27ac_Broad scTIP_Top07 16695 54625 30.6 precision ENCODE_H3K27ac_Broad scTIP_Top07
ENCODE_H3K27ac_Broad scTIP_Top08 16027 54625 29.3 precision ENCODE_H3K27ac_Broad scTIP_Top08
ENCODE_H3K27ac_Broad scTIP_Top09 15925 54625 29.2 precision ENCODE_H3K27ac_Broad scTIP_Top09
ENCODE_H3K27ac_Broad scTIP_Top10 16512 54625 30.2 precision ENCODE_H3K27ac_Broad scTIP_Top10
ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 40868 54625 74.8 precision ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1 48555 54625 88.9 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1 51738 54625 94.7 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2 51545 54625 94.4 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1 38005 54625 69.6 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1 43749 54625 80.1 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1 46710 54625 85.5 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 54625 54625 100.0 precision ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad
scTIP_Top01 ENCODE_H3K27ac_Broad 33794 85789 39.4 recall ENCODE_H3K27ac_Broad scTIP_Top01
scTIP_Top02 ENCODE_H3K27ac_Broad 32066 79798 40.2 recall ENCODE_H3K27ac_Broad scTIP_Top02
scTIP_Top03 ENCODE_H3K27ac_Broad 32400 74075 43.7 recall ENCODE_H3K27ac_Broad scTIP_Top03
scTIP_Top04 ENCODE_H3K27ac_Broad 29010 71959 40.3 recall ENCODE_H3K27ac_Broad scTIP_Top04
scTIP_Top05 ENCODE_H3K27ac_Broad 28087 70197 40.0 recall ENCODE_H3K27ac_Broad scTIP_Top05
scTIP_Top06 ENCODE_H3K27ac_Broad 26962 66581 40.5 recall ENCODE_H3K27ac_Broad scTIP_Top06
scTIP_Top07 ENCODE_H3K27ac_Broad 26803 66262 40.5 recall ENCODE_H3K27ac_Broad scTIP_Top07
scTIP_Top08 ENCODE_H3K27ac_Broad 25486 64282 39.6 recall ENCODE_H3K27ac_Broad scTIP_Top08
scTIP_Top09 ENCODE_H3K27ac_Broad 25355 64743 39.2 recall ENCODE_H3K27ac_Broad scTIP_Top09
scTIP_Top10 ENCODE_H3K27ac_Broad 26476 62684 42.2 recall ENCODE_H3K27ac_Broad scTIP_Top10
H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 30758 71121 43.2 recall ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1
H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad 29293 99494 29.4 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1
H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad 27299 114706 23.8 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1
H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad 28186 110021 25.6 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2
H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad 30942 59688 51.8 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1
H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 28515 65078 43.8 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1
H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad 28346 73246 38.7 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 54625 54625 100.0 recall ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad

ChromHMM annotation of reference peaks found in sample peaks.

Unique: Sample peaks not in Reference peaks

Percentage of sample peaks not found in reference peaks (Reference peakfile: ENCODE_H3K27ac_Broad)

query subject overlap total Percentage type peaklist1 peaklist2
scTIP_Top01 ENCODE_H3K27ac_Broad 51995 85789 60.60 precision scTIP_Top01 ENCODE_H3K27ac_Broad
scTIP_Top02 ENCODE_H3K27ac_Broad 47732 79798 59.80 precision scTIP_Top02 ENCODE_H3K27ac_Broad
scTIP_Top03 ENCODE_H3K27ac_Broad 41675 74075 56.30 precision scTIP_Top03 ENCODE_H3K27ac_Broad
scTIP_Top04 ENCODE_H3K27ac_Broad 42949 71959 59.70 precision scTIP_Top04 ENCODE_H3K27ac_Broad
scTIP_Top05 ENCODE_H3K27ac_Broad 42110 70197 60.00 precision scTIP_Top05 ENCODE_H3K27ac_Broad
scTIP_Top06 ENCODE_H3K27ac_Broad 39619 66581 59.50 precision scTIP_Top06 ENCODE_H3K27ac_Broad
scTIP_Top07 ENCODE_H3K27ac_Broad 39459 66262 59.50 precision scTIP_Top07 ENCODE_H3K27ac_Broad
scTIP_Top08 ENCODE_H3K27ac_Broad 38796 64282 60.40 precision scTIP_Top08 ENCODE_H3K27ac_Broad
scTIP_Top09 ENCODE_H3K27ac_Broad 39388 64743 60.80 precision scTIP_Top09 ENCODE_H3K27ac_Broad
scTIP_Top10 ENCODE_H3K27ac_Broad 36208 62684 57.80 precision scTIP_Top10 ENCODE_H3K27ac_Broad
H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 40363 71121 56.80 precision H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad 70201 99494 70.60 precision H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad 87407 114706 76.20 precision H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad 81835 110021 74.40 precision H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad 28746 59688 48.20 precision H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 36563 65078 56.20 precision H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad 44900 73246 61.30 precision H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 0 54625 0.00 precision ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top01 34881 54625 63.90 recall scTIP_Top01 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top02 35683 54625 65.30 recall scTIP_Top02 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top03 35549 54625 65.10 recall scTIP_Top03 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top04 36903 54625 67.60 recall scTIP_Top04 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top05 37401 54625 68.50 recall scTIP_Top05 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top06 38008 54625 69.60 recall scTIP_Top06 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top07 37930 54625 69.40 recall scTIP_Top07 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top08 38598 54625 70.70 recall scTIP_Top08 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top09 38700 54625 70.80 recall scTIP_Top09 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad scTIP_Top10 38113 54625 69.80 recall scTIP_Top10 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 13757 54625 25.20 recall H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1 6070 54625 11.10 recall H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1 2887 54625 5.29 recall H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2 3080 54625 5.64 recall H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1 16620 54625 30.40 recall H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1 10876 54625 19.90 recall H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1 7915 54625 14.50 recall H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 0 54625 0.00 recall ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad

ChromHMM annotation of sample peaks not found in reference peaks.

Unique: Reference peaks not in Sample peaks

Percentage of reference peaks not found in sample peaks (Reference peakfile: ENCODE_H3K27ac_Broad)

query subject overlap total Percentage type peaklist1 peaklist2
ENCODE_H3K27ac_Broad scTIP_Top01 34881 54625 63.90 precision ENCODE_H3K27ac_Broad scTIP_Top01
ENCODE_H3K27ac_Broad scTIP_Top02 35683 54625 65.30 precision ENCODE_H3K27ac_Broad scTIP_Top02
ENCODE_H3K27ac_Broad scTIP_Top03 35549 54625 65.10 precision ENCODE_H3K27ac_Broad scTIP_Top03
ENCODE_H3K27ac_Broad scTIP_Top04 36903 54625 67.60 precision ENCODE_H3K27ac_Broad scTIP_Top04
ENCODE_H3K27ac_Broad scTIP_Top05 37401 54625 68.50 precision ENCODE_H3K27ac_Broad scTIP_Top05
ENCODE_H3K27ac_Broad scTIP_Top06 38008 54625 69.60 precision ENCODE_H3K27ac_Broad scTIP_Top06
ENCODE_H3K27ac_Broad scTIP_Top07 37930 54625 69.40 precision ENCODE_H3K27ac_Broad scTIP_Top07
ENCODE_H3K27ac_Broad scTIP_Top08 38598 54625 70.70 precision ENCODE_H3K27ac_Broad scTIP_Top08
ENCODE_H3K27ac_Broad scTIP_Top09 38700 54625 70.80 precision ENCODE_H3K27ac_Broad scTIP_Top09
ENCODE_H3K27ac_Broad scTIP_Top10 38113 54625 69.80 precision ENCODE_H3K27ac_Broad scTIP_Top10
ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 13757 54625 25.20 precision ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1 6070 54625 11.10 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1 2887 54625 5.29 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2 3080 54625 5.64 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1 16620 54625 30.40 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1 10876 54625 19.90 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1
ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1 7915 54625 14.50 precision ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 0 54625 0.00 precision ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad
scTIP_Top01 ENCODE_H3K27ac_Broad 51995 85789 60.60 recall ENCODE_H3K27ac_Broad scTIP_Top01
scTIP_Top02 ENCODE_H3K27ac_Broad 47732 79798 59.80 recall ENCODE_H3K27ac_Broad scTIP_Top02
scTIP_Top03 ENCODE_H3K27ac_Broad 41675 74075 56.30 recall ENCODE_H3K27ac_Broad scTIP_Top03
scTIP_Top04 ENCODE_H3K27ac_Broad 42949 71959 59.70 recall ENCODE_H3K27ac_Broad scTIP_Top04
scTIP_Top05 ENCODE_H3K27ac_Broad 42110 70197 60.00 recall ENCODE_H3K27ac_Broad scTIP_Top05
scTIP_Top06 ENCODE_H3K27ac_Broad 39619 66581 59.50 recall ENCODE_H3K27ac_Broad scTIP_Top06
scTIP_Top07 ENCODE_H3K27ac_Broad 39459 66262 59.50 recall ENCODE_H3K27ac_Broad scTIP_Top07
scTIP_Top08 ENCODE_H3K27ac_Broad 38796 64282 60.40 recall ENCODE_H3K27ac_Broad scTIP_Top08
scTIP_Top09 ENCODE_H3K27ac_Broad 39388 64743 60.80 recall ENCODE_H3K27ac_Broad scTIP_Top09
scTIP_Top10 ENCODE_H3K27ac_Broad 36208 62684 57.80 recall ENCODE_H3K27ac_Broad scTIP_Top10
H3K27ac_Diagenode_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 40363 71121 56.80 recall ENCODE_H3K27ac_Broad H3K27ac_Diagenode_pA_Tn5_F10_P9_R1
H3K27ac_Abcam_Tn5_F6_P7_R1 ENCODE_H3K27ac_Broad 70201 99494 70.60 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F6_P7_R1
H3K27ac_Abcam_Tn5_F10_P7_R1 ENCODE_H3K27ac_Broad 87407 114706 76.20 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_Tn5_F10_P7_R1
H3K27ac_Abcam_pA_Tn5_F6_P9_R2 ENCODE_H3K27ac_Broad 81835 110021 74.40 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R2
H3K27ac_Abcam_pA_Tn5_F6_P9_R1 ENCODE_H3K27ac_Broad 28746 59688 48.20 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F6_P9_R1
H3K27ac_Abcam_pA_Tn5_F10_P9_R1 ENCODE_H3K27ac_Broad 36563 65078 56.20 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P9_R1
H3K27ac_Abcam_pA_Tn5_F10_P6_R1 ENCODE_H3K27ac_Broad 44900 73246 61.30 recall ENCODE_H3K27ac_Broad H3K27ac_Abcam_pA_Tn5_F10_P6_R1
ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad 0 54625 0.00 recall ENCODE_H3K27ac_Broad ENCODE_H3K27ac_Broad

ChromHMM annotation of reference peaks not found in sample peaks.

3.2 ChIPseeker

EpiCompare uses ChIPseeker::annotatePeak() to annotate peaks with the nearest gene and genomic regions where the peak is located. The peaks are annotated with genes taken from human genome annotations (hg19 or hg38) provided by Bioconductor.

3.3 Functional Enrichment Analysis

EpiCompare performs KEGG pathway and GO enrichment analysis using clusterProfiler. ChIPseeker::annotatePeak() is first used to assign peaks to nearest genes. Biological themes amongst the genes are identified using ontologies (KEGG and GO). The peaks are annotated with genes taken from annotations of human genome (hg19 or hg38) provided by Bioconductor.

KEGG

GO

3.4 Peak Frequency around TSS

This plots peaks that are mapping to transcriptional start sites (TSS). TSS regions are defined as the flanking sequence of the TSS sites. The frequency of peaks in downstream (-3000bp) and upstream (+3000bp) of TSS is plotted. Faint color line around the main frequency line represents the 95% confidence interval estimated by bootstrap method.

## >> Running bootstrapping for tag matrix...        2022-08-24 18:15:08 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:15:50 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:16:34 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:17:11 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:17:53 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:18:45 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:19:26 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:20:09 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:21:00 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:21:47 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:23:00 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:24:06 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:25:24 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:26:59 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:27:54 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:29:13 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:30:40 
## >> Running bootstrapping for tag matrix...        2022-08-24 18:31:43

4. Session Info

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Monterey 12.5
## 
## Matrix products: default
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggplot2_3.3.6        reshape2_1.4.4       xlsx_0.6.5           rtracklayer_1.56.1   GenomicRanges_1.48.0
##  [6] GenomeInfoDb_1.32.3  IRanges_2.30.0       S4Vectors_0.34.0     BiocGenerics_0.42.0  EpiCompare_1.1.1    
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2                               tidyselect_1.1.2                        
##   [3] RSQLite_2.2.16                           AnnotationDbi_1.58.0                    
##   [5] htmlwidgets_1.5.4                        grid_4.2.1                              
##   [7] BiocParallel_1.30.3                      scatterpie_0.1.7                        
##   [9] munsell_0.5.0                            ragg_1.2.2                              
##  [11] codetools_0.2-18                         withr_2.5.0                             
##  [13] colorspace_2.0-3                         GOSemSim_2.22.0                         
##  [15] TxDb.Hsapiens.UCSC.hg38.knownGene_3.15.0 Biobase_2.56.0                          
##  [17] filelock_1.0.2                           highr_0.9                               
##  [19] knitr_1.39                               rstudioapi_0.13                         
##  [21] rJava_1.0-6                              DOSE_3.22.0                             
##  [23] labeling_0.4.2                           MatrixGenerics_1.8.1                    
##  [25] GenomeInfoDbData_1.2.8                   polyclip_1.10-0                         
##  [27] seqPattern_1.28.0                        bit64_4.0.5                             
##  [29] farver_2.1.1                             downloader_0.4                          
##  [31] vctrs_0.4.1                              treeio_1.20.2                           
##  [33] generics_0.1.3                           xfun_0.32                               
##  [35] BiocFileCache_2.4.0                      R6_2.5.1                                
##  [37] graphlayouts_0.8.1                       locfit_1.5-9.6                          
##  [39] bitops_1.0-7                             BRGenomics_1.8.0                        
##  [41] cachem_1.0.6                             fgsea_1.22.0                            
##  [43] gridGraphics_0.5-1                       DelayedArray_0.22.0                     
##  [45] assertthat_0.2.1                         vroom_1.5.7                             
##  [47] promises_1.2.0.1                         BiocIO_1.6.0                            
##  [49] scales_1.2.0                             ggraph_2.0.6                            
##  [51] enrichplot_1.16.1                        gtable_0.3.0                            
##  [53] tidygraph_1.2.1                          rlang_1.0.4                             
##  [55] genefilter_1.78.0                        systemfonts_1.0.4                       
##  [57] splines_4.2.1                            lazyeval_0.2.2                          
##  [59] impute_1.70.0                            BiocManager_1.30.18                     
##  [61] yaml_2.3.5                               crosstalk_1.2.0                         
##  [63] GenomicFeatures_1.48.3                   httpuv_1.6.5                            
##  [65] qvalue_2.28.0                            clusterProfiler_4.4.4                   
##  [67] tools_4.2.1                              ggplotify_0.1.0                         
##  [69] gridBase_0.4-7                           ellipsis_0.3.2                          
##  [71] gplots_3.1.3                             jquerylib_0.1.4                         
##  [73] RColorBrewer_1.1-3                       Rcpp_1.0.9                              
##  [75] plyr_1.8.7                               progress_1.2.2                          
##  [77] zlibbioc_1.42.0                          purrr_0.3.4                             
##  [79] RCurl_1.98-1.8                           prettyunits_1.1.1                       
##  [81] viridis_0.6.2                            SummarizedExperiment_1.26.1             
##  [83] ggrepel_0.9.1                            magrittr_2.0.3                          
##  [85] data.table_1.14.2                        DO.db_2.9                               
##  [87] matrixStats_0.62.0                       xlsxjars_0.6.1                          
##  [89] hms_1.1.1                                patchwork_1.1.1                         
##  [91] mime_0.12                                evaluate_0.16                           
##  [93] xtable_1.8-4                             XML_3.99-0.10                           
##  [95] gridExtra_2.3                            compiler_4.2.1                          
##  [97] biomaRt_2.52.0                           tibble_3.1.8                            
##  [99] KernSmooth_2.23-20                       crayon_1.5.1                            
## [101] shadowtext_0.1.2                         htmltools_0.5.3                         
## [103] ggfun_0.0.6                              later_1.3.0                             
## [105] tzdb_0.3.0                               tidyr_1.2.0                             
## [107] geneplotter_1.74.0                       aplot_0.1.6                             
## [109] DBI_1.1.3                                tweenr_2.0.0                            
## [111] ChIPseeker_1.32.0                        genomation_1.28.0                       
## [113] dbplyr_2.2.1                             MASS_7.3-58.1                           
## [115] rappdirs_0.3.3                           boot_1.3-28                             
## [117] Matrix_1.4-1                             readr_2.1.2                             
## [119] cli_3.3.0                                parallel_4.2.1                          
## [121] igraph_1.3.4                             pkgconfig_2.0.3                         
## [123] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  GenomicAlignments_1.32.1                
## [125] plotly_4.10.0                            xml2_1.3.3                              
## [127] ggtree_3.4.2                             annotate_1.74.0                         
## [129] bslib_0.4.0                              XVector_0.36.0                          
## [131] yulab.utils_0.0.5                        stringr_1.4.0                           
## [133] digest_0.6.29                            Biostrings_2.64.0                       
## [135] rmarkdown_2.15                           fastmatch_1.1-3                         
## [137] tidytree_0.4.0                           restfulr_0.0.15                         
## [139] curl_4.3.2                               shiny_1.7.2                             
## [141] Rsamtools_2.12.0                         gtools_3.9.3                            
## [143] rjson_0.2.21                             lifecycle_1.0.1                         
## [145] nlme_3.1-159                             jsonlite_1.8.0                          
## [147] viridisLite_0.4.0                        BSgenome_1.64.0                         
## [149] fansi_1.0.3                              pillar_1.8.0                            
## [151] lattice_0.20-45                          KEGGREST_1.36.3                         
## [153] fastmap_1.1.0                            httr_1.4.4                              
## [155] plotrix_3.8-2                            survival_3.4-0                          
## [157] GO.db_3.15.0                             interactiveDisplayBase_1.34.0           
## [159] glue_1.6.2                               UpSetR_1.4.0                            
## [161] png_0.1-7                                BiocVersion_3.15.2                      
## [163] bit_4.0.4                                sass_0.4.2                              
## [165] ggforce_0.3.4                            stringi_1.7.8                           
## [167] blob_1.2.3                               textshaping_0.3.6                       
## [169] org.Hs.eg.db_3.15.0                      DESeq2_1.36.0                           
## [171] AnnotationHub_3.4.0                      caTools_1.18.2                          
## [173] memoise_2.0.1                            dplyr_1.0.9                             
## [175] ape_5.6-2